On Fri, Mar 30, 2012 at 5:54 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Fri, Mar 30, 2012 at 8:42 AM, Kathi Zarnack <zarnack@ebi.ac.uk> wrote:
> > Hi,
> > I think you have to add vector() to strand(ga), since the strand
> information
> > comes as Rle which does not work in the ifelse() test directly. At least
> > this is my experience with GRanges objects.
>
> It's true that sometimes you get bitten by Rle's popping up where you
> didn't expect them when you try and index things and need to do some
> as.vector() mojo here and there, but in this case it should actually
> work (depending on your version of R/bioc, I guess).
>
> In my case (running R-2.15 RC), the Rle "surprise" doesn't catch you
> here, but it's still a good idea to keep in mind.
>
>
Thanks, Steve. ifelse() has worked on Rle for a very long time. Btw, this
issue usually comes up when trying to extract from an ordinary vector with
[. Since we can't / don't want to define methods on base generics for base
data structures, we need to define new generics. In the case of [, one can
use seqselect() as an alternative.

Thanks for pointing that out!
>
> -steve
>
> > Best regards,
> > Kathi
> >
> >
> > On 30/03/12 13:37, Steve Lianoglou wrote:
> >>
> >> Hi,
> >>
> >> On Fri, Mar 30, 2012 at 6:04 AM, Stefanie<stefanie.tauber@univie.ac.at>
> >>  wrote:
> >>>
> >>> Dear list,
> >>>
> >>> having a GappedAlignments or GRangesList object at hand,
> >>> what is the quickest way to flip strand signs?
> >>>
> >>> So for each entry, I want to flip "-" to "+" and vice versa.
> >>
> >> Let's assume that your GappedAlignments object is called `ga`, I think
> >> this should work, no?
> >>
> >> R>  strand(ga)<- ifelse(strand(ga) == '+', '-', '+')
> >>
> >> To the devs:
> >>
> >> For some reason, `example(GappedAlignments)` is throwing the following
> >> error on me, so I can't actually test at the moment:
> >>
> >> Error in elementLengths(rglist(x)) :
> >>   error in evaluating the argument 'x' in selecting a method for
> >> function 'elementLengths': Error in .Call(.NAME, ..., PACKAGE =
> >> PACKAGE) :
> >>   Incorrect number of arguments (6), expecting 4 for
> >> 'cigar_to_list_of_IRanges_by_alignment'
> >>
> >> sessionInfo() pasted below.
> >>
> >> HTH,
> >>
> >> -steve
> >>
> >> R version 2.15.0 RC (2012-03-24 r58823)
> >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> >>
> >> locale:
> >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >> [1] Rsamtools_1.7.41     Biostrings_2.23.6    GenomicRanges_1.7.40
> >> [4] IRanges_1.13.34      BiocGenerics_0.1.14
> >>
> >
> > --
> > Dr. Kathi Zarnack
> > Luscombe Group
> > European Bioinformatics Institute
> > Wellcome Trust Genome Campus
> > Hinxton, Cambridge
> > CB10 1SD, UK
> > tel +44 1223 494 526
> >
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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